@Bagzerg protoc needs to know where to look for shared libraries. (It cannot search your whole system). This is similar to how PATH helps in locating executables. See this post here that explains LD_LIBRARY_PATH.
– Kshitiz SharmaFeb 18 '15 at 13:29

This cleans the current installation and installs protobuf at /usr
Run ldconfig to update ld.so.cache after making sure that /usr/local/lib is listed in /etc/ld.so.conf. i.e.
Edit /etc/ld.so.conf and append /usr/local/lib to it and run ldconfig